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Hu S, Han P, Wang BT, Jin L, Ruan HH, Jin FJ. Transcriptome-wide analysis of a superior xylan degrading isolate Penicillium oxalicum 5-18 revealed active lignocellulosic degrading genes. Arch Microbiol 2024; 206:327. [PMID: 38922442 DOI: 10.1007/s00203-024-04063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
Lignocellulose biomass raw materials have a high value in energy conversion. Recently, there has been growing interest in using microorganisms to secret a series of enzymes for converting low-cost biomass into high-value products such as biofuels. We previously isolated a strain of Penicillium oxalicun 5-18 with promising lignocellulose-degrading capability. However, the mechanisms of lignocellulosic degradation of this fungus on various substrates are still unclear. In this study, we performed transcriptome-wide profiling and comparative analysis of strain 5-18 cultivated in liquid media with glucose (Glu), xylan (Xyl) or wheat bran (WB) as sole carbon source. In comparison to Glu culture, the number of differentially expressed genes (DEGs) induced by WB and Xyl was 4134 and 1484, respectively, with 1176 and 868 genes upregulated. Identified DEGs were enriched in many of the same pathways in both comparison groups (WB vs. Glu and Xly vs. Glu). Specially, 118 and 82 CAZyme coding genes were highly upregulated in WB and Xyl cultures, respectively. Some specific pathways including (Hemi)cellulose metabolic processes were enriched in both comparison groups. The high upregulation of these genes also confirmed the ability of strain 5-18 to degrade lignocellulose. Co-expression and co-upregulated of genes encoding CE and AA CAZy families, as well as other (hemi)cellulase revealed a complex degradation strategy in this strain. Our findings provide new insights into critical genes, key pathways and enzyme arsenal involved in the biomass degradation of P. oxalicum 5-18.
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Affiliation(s)
- Shuang Hu
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Pei Han
- Key Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, China
| | - Bao-Teng Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Long Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Hua Ruan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China.
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2
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Tong L, Li Y, Lou X, Wang B, Jin C, Fang W. Powerful cell wall biomass degradation enzymatic system from saprotrophic Aspergillus fumigatus. Cell Surf 2024; 11:100126. [PMID: 38827922 PMCID: PMC11143905 DOI: 10.1016/j.tcsw.2024.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
Cell wall biomass, Earth's most abundant natural resource, holds significant potential for sustainable biofuel production. Composed of cellulose, hemicellulose, lignin, pectin, and other polymers, the plant cell wall provides essential structural support to diverse organisms in nature. In contrast, non-plant species like insects, crustaceans, and fungi rely on chitin as their primary structural polysaccharide. The saprophytic fungus Aspergillus fumigatus has been widely recognized for its adaptability to various environmental conditions. It achieves this by secreting different cell wall biomass degradation enzymes to obtain essential nutrients. This review compiles a comprehensive collection of cell wall degradation enzymes derived from A. fumigatus, including cellulases, hemicellulases, various chitin degradation enzymes, and other polymer degradation enzymes. Notably, these enzymes exhibit biochemical characteristics such as temperature tolerance or acid adaptability, indicating their potential applications across a spectrum of industries.
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Affiliation(s)
- Lige Tong
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Yunaying Li
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Baoding, Hebei, China
| | - Xinke Lou
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Baoding, Hebei, China
| | - Bin Wang
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Cheng Jin
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenxia Fang
- National Key Laboratory of Non-food Biomass Energy Technology, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi, China
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3
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Khatri S, Chaudhary P, Shivay YS, Sharma S. Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field. MICROBIAL ECOLOGY 2023; 86:2047-2059. [PMID: 37010558 DOI: 10.1007/s00248-023-02211-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.
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Affiliation(s)
- Shivani Khatri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Priya Chaudhary
- UQ-IITD Academy of Research, IIT Delhi, New Delhi, 110016, India
| | - Yashbir S Shivay
- Division of Agronomy, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
- UQ-IITD Academy of Research, IIT Delhi, New Delhi, 110016, India.
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4
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Jiang S, Zhou Z, Han J, Fan Q, Long Z, Wang J. Enhanced enzyme thermostability of a family I.3 lipase LipSR1 by T118A mutation at the calcium-binding site. Biotechnol Lett 2023; 45:1199-1207. [PMID: 37439931 DOI: 10.1007/s10529-023-03413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/24/2023] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
OBJECTIVES The lipase gene lipSR1 isolated from oil-contaminated soil exhibits high hydrolytic activity for short-chain fatty acid substrates. A single calcium ion is required to anchor the lid of LipSR1 in an open conformation by coordination with two aspartate residues and three other residues in the lid. The lid of LipSR1 is anchored by Ca2+, which is coordinated by side-chain carboxyl oxygens of Asp153 and Asp157, carbonyl oxygens of Thr118 and Ser144, and the side chain of Gln120. RESULTS D157A, D153R, Q120A, S144A, and T118A mutants were produced by site-directed mutagenesis in this study. Analyses of hydrolytic activity and thermostability showed that the properties of D157A, D153R, Q120A, and S144A were almost lost, suggesting that Asp157, Asp153, Gln120, and Ser144 are important residues for LipSR1. However, the catalytic performance of T118A was clearly maintained. Moreover, the thermostability of mutant T118A was higher than that of wild-type LipSR1. CONCLUSIONS These results indicated that mutation of threonine at position 118 improved the stability of the enzyme at high temperature.
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Affiliation(s)
- Shijie Jiang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qingfeng Fan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Zhijian Long
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Jin Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Dwyer K, Bentley IS, Fitzpatrick DA, Saleh AA, Tighe E, McGleenan E, Gaffney D, Walsh G. Recombinant production, characterization and industrial application testing of a novel acidic exo/endo-chitinase from Rasamsonia emersonii. Extremophiles 2023; 27:10. [PMID: 37071215 DOI: 10.1007/s00792-023-01293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/08/2023] [Indexed: 04/19/2023]
Abstract
An acid-active exo/endo-chitinase; comprising a GH18 catalytic domain and substrate insertion domain; originating from the thermophilic filamentous fungus Rasamsonia emersonii, was expressed in Pichia pastoris. In silico analysis including phylogenetic analysis, and recombinant production, purification, biochemical characterisation, and industrial application testing, was carried out. The expressed protein was identified by SDS-PAGE as a smear from 56.3 to 125.1 kDa, which sharpens into bands at 46.0 kDa, 48.4 kDa and a smear above 60 kDa when treated with PNGase F. The acid-active chitinase was primarily a chitobiosidase but displayed some endo-chitinase and acetyl-glucosamidase activity. The enzyme was optimally active at 50 °C, and markedly low pH of 2.8. As far as the authors are aware, this is the lowest pH optima reported for any fungal chitinase. The acid-active chitinase likely plays a role in chitin degradation for cell uptake in its native environment, perhaps in conjunction with a chitin deacetylase. Comparative studies with other R. emersonii chitinases indicate that they may play a synergistic role in this. The acid-active chitinase displayed some efficacy against non-treated substrates; fungal chitin and chitin from shrimp. Thus, it may be suited to industrial chitin hydrolysis reactions for extraction of glucosamine and chitobiose at low pH.
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Affiliation(s)
- Kelly Dwyer
- MBio Labs at Monaghan Mushrooms Ireland Ultd, Tyholland, Monaghan, Ireland.
- Chemical Sciences Department, University of Limerick, Castletroy, Limerick, Ireland.
| | - Ian S Bentley
- MBio Labs at Monaghan Mushrooms Ireland Ultd, Tyholland, Monaghan, Ireland
| | | | - Aliabbas A Saleh
- MBio Labs at Monaghan Mushrooms Ireland Ultd, Tyholland, Monaghan, Ireland
| | - Emma Tighe
- MBio Labs at Monaghan Mushrooms Ireland Ultd, Tyholland, Monaghan, Ireland
| | - Eibhilin McGleenan
- MBio Labs at Monaghan Mushrooms Ireland Ultd, Tyholland, Monaghan, Ireland
| | - Darragh Gaffney
- MBio Labs at Monaghan Mushrooms Ireland Ultd, Tyholland, Monaghan, Ireland
| | - Gary Walsh
- Chemical Sciences Department, University of Limerick, Castletroy, Limerick, Ireland.
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6
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Aktas C, Ruzgar D, Gurkok S, Gormez A. Purification and characterization of Stenotrophomonas maltophilia chitinase with antifungal and insecticidal properties. Prep Biochem Biotechnol 2022:1-10. [PMID: 36369794 DOI: 10.1080/10826068.2022.2142942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study aimed to determine the ability of bacteria to produce the chitinase enzyme, purify, and characterize the enzyme from the isolate with the best activity, and determine the use of this purified enzyme as a biocontrol agent. The chitinolytic bacterium was identified as Stenotrophomonas maltophilia. The chitinase enzyme was purified 1.4 times at a 30% ammonium sulfate concentration with a yield of 40.7%. Following partial purification, the enzyme was purified by ion-exchange chromatography using HiPrep Q XL 16/10 column and HiPrep™ 26/10 desalting column with 25.34% and 18.12% yields, respectively. It was calculated that the purified enzyme had a molecular weight of 52 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The optimum activity of the enzyme was determined at 50 °C and pH 7.0. Enzyme activity was most induced by Fe2+, while it was most inhibited by Zn2+ at 5 mM concentration. Km and Vmax values of the enzyme for colloidal chitin were calculated as 1.6419 mg/mL and 16.129 U/mg, respectively. The purified chitinase was used as a biocontrol agent against the fungus Fusarium oxysporum and potato beetle Leptinotarsa decemlineata. The enzyme was shown to be effective in reducing the growth of fungus and causing disruption of the chitin structure of potato beetle.
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Affiliation(s)
- Cigdem Aktas
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Damla Ruzgar
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Sumeyra Gurkok
- Department of Biology, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Arzu Gormez
- Department of Biology, Faculty of Science, Dokuz Eylul University, İzmir, Turkey
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7
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Ortega N, Sáez L, Palacios D, Busto MD. Kinetic Modeling, Thermodynamic Approach and Molecular Dynamics Simulation of Thermal Inactivation of Lipases from Burkholderia cepacia and Rhizomucor miehei. Int J Mol Sci 2022; 23:ijms23126828. [PMID: 35743268 PMCID: PMC9224459 DOI: 10.3390/ijms23126828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
The behavior against temperature and thermal stability of enzymes is a topic of importance for industrial biocatalysis. This study focuses on the kinetics and thermodynamics of the thermal inactivation of Lipase PS from B. cepacia and Palatase from R. miehei. Thermal inactivation was investigated using eight inactivation models at a temperature range of 40–70 °C. Kinetic modeling showed that the first-order model and Weibull distribution were the best equations to describe the residual activity of Lipase PS and Palatase, respectively. The results obtained from the kinetic parameters, decimal reduction time (D and tR), and temperature required (z and z’) indicated a higher thermal stability of Lipase PS compared to Palatase. The activation energy values (Ea) also indicated that higher energy was required to denature bacterial (34.8 kJ mol−1) than fungal (23.3 kJ mol−1) lipase. The thermodynamic inactivation parameters, Gibbs free energy (ΔG#), entropy (ΔS#), and enthalpy (ΔH#) were also determined. The results showed a ΔG# for Palatase (86.0–92.1 kJ mol−1) lower than for Lipase PS (98.6–104.9 kJ mol−1), and a negative entropic and positive enthalpic contribution for both lipases. A comparative molecular dynamics simulation and structural analysis at 40 °C and 70 °C were also performed.
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Rajput M, Kumar M, Pareek N. Myco-chitinases as versatile biocatalysts for translation of coastal residual resources to eco-competent chito-bioactives. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Anwar S, DasGupta D, Shafie A, Alhumaydhi FA, Alsagaby SA, Shahwan M, Anjum F, Al Abdulmonem W, Sharaf SE, Imtaiyaz Hassan M. Implications of tempol in pyruvate dehydrogenase kinase 3 targeted anticancer therapeutics: Computational, spectroscopic, and calorimetric studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118581] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Naeem M, Manzoor S, Abid MUH, Tareen MBK, Asad M, Mushtaq S, Ehsan N, Amna D, Xu B, Hazafa A. Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review. J Fungi (Basel) 2022; 8:jof8020109. [PMID: 35205863 PMCID: PMC8875690 DOI: 10.3390/jof8020109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.
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Affiliation(s)
- Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang 050025, China;
| | - Saba Manzoor
- Department of Zoology, University of Sialkot, Sialkot 51310, Pakistan;
| | | | | | - Mirza Asad
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot 51040, Pakistan;
| | - Nazia Ehsan
- Department of Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Dua Amna
- Institute of Food Science & Nutrition, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University (BNU-HKBU) United International College, Zhuhai 519087, China
- Correspondence: (B.X.); (A.H.)
| | - Abu Hazafa
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
- Correspondence: (B.X.); (A.H.)
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11
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Thermotolerance and Adaptation to Climate Change. Fungal Biol 2022. [DOI: 10.1007/978-3-030-89664-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Poria V, Rana A, Kumari A, Grewal J, Pranaw K, Singh S. Current Perspectives on Chitinolytic Enzymes and Their Agro-Industrial Applications. BIOLOGY 2021; 10:1319. [PMID: 34943233 PMCID: PMC8698876 DOI: 10.3390/biology10121319] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022]
Abstract
Chitinases are a large and diversified category of enzymes that break down chitin, the world's second most prevalent polymer after cellulose. GH18 is the most studied family of chitinases, even though chitinolytic enzymes come from a variety of glycosyl hydrolase (GH) families. Most of the distinct GH families, as well as the unique structural and catalytic features of various chitinolytic enzymes, have been thoroughly explored to demonstrate their use in the development of tailor-made chitinases by protein engineering. Although chitin-degrading enzymes may be found in plants and other organisms, such as arthropods, mollusks, protozoans, and nematodes, microbial chitinases are a promising and sustainable option for industrial production. Despite this, the inducible nature, low titer, high production expenses, and susceptibility to severe environments are barriers to upscaling microbial chitinase production. The goal of this study is to address all of the elements that influence microbial fermentation for chitinase production, as well as the purifying procedures for attaining high-quality yield and purity.
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Affiliation(s)
- Vikram Poria
- Department of Microbiology, Central University of Haryana, Mahendargarh 123031, India; (V.P.); (A.K.)
| | - Anuj Rana
- Department of Microbiology (COBS & H), CCS Haryana Agricultural University, Hisar 125004, India;
| | - Arti Kumari
- Department of Microbiology, Central University of Haryana, Mahendargarh 123031, India; (V.P.); (A.K.)
| | - Jasneet Grewal
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa, 102-096 Warsaw, Poland; (J.G.); (K.P.)
| | - Kumar Pranaw
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa, 102-096 Warsaw, Poland; (J.G.); (K.P.)
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendargarh 123031, India; (V.P.); (A.K.)
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13
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Anwar S, Khan S, Anjum F, Shamsi A, Khan P, Fatima H, Shafie A, Islam A, Hassan MI. Myricetin inhibits breast and lung cancer cells proliferation via inhibiting MARK4. J Cell Biochem 2021; 123:359-374. [PMID: 34751461 DOI: 10.1002/jcb.30176] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/09/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022]
Abstract
Identifying novel molecules as potential kinase inhibitors are gaining significant attention globally. The present study suggests Myricetin as a potential inhibitor of microtubule-affinity regulating kinase (MARK4), adding another molecule to the existing list of anticancer therapeutics. MARK4 regulates initial cell division steps and is a potent druggable target for various cancers. Structure-based docking with 100 ns molecular dynamics simulation depicted activity of Myricetin in the active site pocket of MARK4 and the formation of a stable complex. The fluorescence-based assay showed excellent affinity of Myricetin to MARK4 guided by static and dynamic quenching. Moreover, the assessment of enthalpy change (∆H) and entropy change (∆S) delineated electrostatic interactions as a dominant force in the MARK4-myricetin interaction. Isothermal titration calorimetric measurements revealed spontaneous binding of Myricetin with MARK4. Further, the kinase assay depicted significant inhibition of MARK4 by Myricetin with IC50 = 3.11 µM. Additionally, cell proliferation studies established that Myricetin significantly inhibited the cancer cells (MCF-7 and A549) proliferation, and inducing apoptosis. This study provides a solid rationale for developing Myricetin as a promising anticancer molecule in the MARK4 mediated malignancies.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shama Khan
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, South Africa
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Hera Fatima
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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14
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Recombinant production and characterisation of two chitinases from Rasamsonia emersonii, and assessment of their potential industrial applicability. Appl Microbiol Biotechnol 2021; 105:7769-7783. [PMID: 34581845 DOI: 10.1007/s00253-021-11578-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022]
Abstract
Rasamsonia emersonii (previously Talaromyces emersonii) is a thermophilic filamentous fungus displaying optimum growth at 45 °C. It has a history of use in commercial food enzyme production. Its unfractionated chitinolytic secretome was partially characterised in the early 1990s; however, no individual chitinase from this source has been described in literature previously. This study describes two GH18 chitinases originating from the R. emersonii genome, expressed in the methylotrophic yeast P. pastoris. Chit1 comprises of a GH18 catalytic domain and Chit2 comprises of a GH18 catalytic domain and a chitin-binding motif at the C-terminal. The chitinases were expressed as glycoproteins. The apparent molecular weight of Chit1 was 35.8-42.1 kDa with a smearing tail associated with glyco-sidechains visible up to 72.2 kDa. This became two bands of 30.8 and 29.0 kDa upon de-glycosylation. The apparent molecular weight of Chit2 was 50.4 kDa, reducing to 48.2 kDa upon de-glycosylation. Both chitinases displayed endo-chitinase and chitobiosidase activity, temperature optima of 50-55 °C and low pH optima (pH 4.5 or lower); Chit1 displayed a pH optimum of 3.5, retaining > 60% maximum activity at pH 2.2, a pH range lower than most enzymes of fungal origin. Chit2 displayed the highest chitin-degrading ability at 3456 µmol/mg on 4-NP-triacetylchitotriose, but lost activity faster than Chit1, which displayed 403 µmol/mg on the same substrate. The predicted D values (time required to reduce the enzyme activity to 10% of its original value at 50 °C) were 19.2 and 2.3 days for Chit1 and Chit2, respectively. Thus, Chit1 can be considered one of few hyperthermostable chitinase enzymes described in literature to date. Their physicochemical properties render these chitinases likely suitable for shrimp chitin processing including one-step chitin hydrolysis and alternative sustainable protein processing and the attractive emerging application of mushroom food waste valorisation.Key points• Two GH18 chitinases originating from the industrially relevant thermophilic fungus R. emersonii were cloned and expressed in P. pastoris.• The purified recombinant chitinases showed low pH and high temperature optima and appreciable thermostability at industrially relevant temperatures.• The chitinases displayed characteristics that indicate their likely suitability to several industrial applications including sustainable alternative protein processing, food waste valorisation of commercial mushroom production and one-step shrimp chitin processing.
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Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.
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Bhagwat P, Amobonye A, Singh S, Pillai S. A comparative analysis of GH18 chitinases and their isoforms from Beauveria bassiana: An in-silico approach. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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Chitinase production by Trichoderma koningiopsis UFSMQ40 using solid state fermentation. Braz J Microbiol 2020; 51:1897-1908. [PMID: 32737868 DOI: 10.1007/s42770-020-00334-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
The chitinases have extensive biotechnological potential but have been little exploited commercially due to the low number of good chitinolytic microorganisms. The purpose of this study was to identify a chitinolytic fungal and optimize its production using solid state fermentation (SSF) and agroindustry substrate, to evaluate different chitin sources for chitinase production, to evaluate different solvents for the extraction of enzymes produced during fermentation process, and to determine the nematicide effect of enzymatic extract and biological control of Meloidogyne javanica and Meloidogyne incognita nematodes. The fungus was previously isolated from bedbugs of Tibraca limbativentris Stal (Hemiptera: Pentatomidae) and selected among 51 isolated fungal as the largest producer of chitinolytic enzymes in SSF. The isolate UFSMQ40 has been identified as Trichoderma koningiopsis by the amplification of tef1 gene fragments. The greatest chitinase production (10.76 U gds-1) occurred with wheat bran substrate at 55% moisture, 15% colloidal chitin, 100% of corn steep liquor, and two discs of inoculum at 30 °C for 72 h. Considering the enzymatic inducers, the best chitinase production by the isolated fungus was achieved using chitin in colloidal, powder, and flakes. The usage of 1:15 g/mL of sodium citrate-phosphate buffer was the best ratio for chitinase extraction of SSF. The Trichoderma koningiopsis UFSMQ40 showed high mortality of M. javanica and M. incognita when applied to treatments with enzymatic filtrated and the suspension of conidia.
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Amir M, Ahamad S, Mohammad T, Jairajpuri DS, Hasan GM, Dohare R, Islam A, Ahmad F, Hassan MI. Investigation of conformational dynamics of Tyr89Cys mutation in protection of telomeres 1 gene associated with familial melanoma. J Biomol Struct Dyn 2019; 39:35-44. [DOI: 10.1080/07391102.2019.1705186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Mohd. Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shahzaib Ahamad
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Moradabad, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Kingdom of Saudi Arabia
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability. N Biotechnol 2019; 53:65-72. [DOI: 10.1016/j.nbt.2019.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/24/2019] [Accepted: 07/07/2019] [Indexed: 01/05/2023]
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21
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Synthesis, homology modeling, molecular docking, dynamics, and antifungal screening of new 4-hydroxycoumarin derivatives as potential chitinase inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.11.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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22
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Kumar A, Khan FI, Olaniran AO. Chloroacetaldehyde dehydrogenase from Ancylobacter aquaticus UV5: Cloning, expression, characterization and molecular modeling. Int J Biol Macromol 2018; 114:1117-1126. [PMID: 29605256 DOI: 10.1016/j.ijbiomac.2018.03.176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 08/07/2017] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
1,2-Dichloroethane (1,2-DCE) is oxidatively converted to a carcinogenic intermediate compound, chloroacetaldehyde by chloroacetaldehyde dehydrogenase (CAldA) during its biodegradation by many bacterial strains, including Xanthobacter autotrophicus and Ancylobacter aquaticus. In this study, a 55kDa NAD-dependent CAldA expressed by chromosomally encoded aldA gene, is reported in an indigenous Ancylobacter aquaticus UV5. A. aquaticus UV5 aldA gene was found to be 99% homologous to the plasmid (pXAU1) encoded aldA gene reported in X. autotrophicus GJ10. Pulse-field gel electrophoresis (PFGE) and PCR experiments revealed the absence of pXAU1 in A. aquaticus UV5 and that aldA was chromosomal encoded. A 6× His-tag fused CAldA cloned in pET15b, overexpressed and purified on Co-agarose affinity column using AKTA purification system showed Mr of 57,526. CAldA was active optimally at pH9 and 30°C. The Km and vmax for the substrate, acetaldehyde were found to be 115μM and 650mU/mg, respectively. CAldA substrate specificity was found to be low for chloroacetaldehyde, formaldehyde, propionaldehyde, butyraldehyde, benzaldehyde and glutaraldehyde as compared to acetaldehyde. Computational modeling revealed a predicted structure of CAldA consisting of five β-sheets that comprise seven antiparallel β-strands and 11 mix strands. The Molecular Dynamics and Docking studies showed that acetaldehyde bind to CaldA more tightly as compared to chloroacetaldehyde.
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Affiliation(s)
- Ajit Kumar
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown 6139, South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa.
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Sosnowska ME, Jankiewicz U, Kutwin M, Chwalibog A, Gałązka A. Influence of salts and metal nanoparticles on the activity and thermal stability of a recombinant chitinase from Stenotrophomonas maltophilia N4. Enzyme Microb Technol 2018; 116:6-15. [PMID: 29887018 DOI: 10.1016/j.enzmictec.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/08/2018] [Accepted: 05/04/2018] [Indexed: 11/28/2022]
Abstract
Cells of Escherichia coli Rosetta, containing plasmid pET-28a with sequences of DNA of chitinase from Stenotrophomonas maltophilia N4, were used for the efficient synthesis of recombinant chitinolytic enzyme. The objective of this study was to improve thermal stability of the recombinant chitinase by salts and metal nanoparticles (NP). The studied chitinase was thermolabile and largely lost its activity in the first minutes of storage at 50 and 60 °C. The optimum temperature for colloidal chitin hydrolysis by the enzyme was 50 °C. Application of sodium aurothiomalate hydrate and manganese chloride enhanced the activity of the recombinant enzyme. In general, chitinase activity was higher when silver nanoparticles (Ag-NP) were used, but lower for other NP. The thermal stability of chitinase immobilized on Ag-NP and manganese chloride was significantly higher than that of free chitinase. Chitinase thermal stability after gold and manganese oxide nanoparticle application was higher than that of the control at 50 °C. Platinum nanoparticles had no significant effect on thermostability. The Ag-NP had a smaller diameter (from 2 to 20 nm) than Au-NP (from 5 to 70 nm) and Pt-NP (from 4 to 80 nm). The TEM analysis showed that the used NP had a higher affinity for chitinase than for the synthetic substrate. The type, size, and location of the NP on the enzyme played a major role in the thermal stability of chitinase.
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Affiliation(s)
- Malwina Ewa Sosnowska
- Department of Animal Nutrition and Biotechnology, Warsaw University of Life Sciences, Ciszewskiego 8, Warsaw, 02-786 Poland; Department of Biochemistry, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776 Poland
| | - Urszula Jankiewicz
- Department of Biochemistry, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776 Poland
| | - Marta Kutwin
- Department of Animal Nutrition and Biotechnology, Warsaw University of Life Sciences, Ciszewskiego 8, Warsaw, 02-786 Poland
| | - André Chwalibog
- Department of Veterinary and Animal Sciences, University of Copenhagen, Groennegaardsvej 3, 1870 Frederiksberg, Denmark.
| | - Agnieszka Gałązka
- Department of Biochemistry, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776 Poland
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Kidibule PE, Santos-Moriano P, Jiménez-Ortega E, Ramírez-Escudero M, Limón MC, Remacha M, Plou FJ, Sanz-Aparicio J, Fernández-Lobato M. Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity. Microb Cell Fact 2018; 17:47. [PMID: 29566690 PMCID: PMC5863366 DOI: 10.1186/s12934-018-0895-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/17/2018] [Indexed: 11/30/2022] Open
Abstract
Background Chitinases are ubiquitous enzymes that have gained a recent biotechnological attention due to their ability to transform biological waste from chitin into valued chito-oligomers with wide agricultural, industrial or medical applications. The biological activity of these molecules is related to their size and acetylation degree. Chitinase Chit42 from Trichoderma harzianum hydrolyses chitin oligomers with a minimal of three N-acetyl-d-glucosamine (GlcNAc) units. Gene chit42 was previously characterized, and according to its sequence, the encoded protein included in the structural Glycoside Hydrolase family GH18. Results Chit42 was expressed in Pichia pastoris using fed-batch fermentation to about 3 g/L. Protein heterologously expressed showed similar biochemical properties to those expressed by the natural producer (42 kDa, optima pH 5.5–6.5 and 30–40 °C). In addition to hydrolyse colloidal chitin, this enzyme released reducing sugars from commercial chitosan of different sizes and acetylation degrees. Chit42 hydrolysed colloidal chitin at least 10-times more efficiently (defined by the kcat/Km ratio) than any of the assayed chitosan. Production of partially acetylated chitooligosaccharides was confirmed in reaction mixtures using HPAEC-PAD chromatography and mass spectrometry. Masses corresponding to (d-glucosamine)1–8-GlcNAc were identified from the hydrolysis of different substrates. Crystals from Chit42 were grown and the 3D structure determined at 1.8 Å resolution, showing the expected folding described for other GH18 chitinases, and a characteristic groove shaped substrate-binding site, able to accommodate at least six sugar units. Detailed structural analysis allows depicting the features of the Chit42 specificity, and explains the chemical nature of the partially acetylated molecules obtained from analysed substrates. Conclusions Chitinase Chit42 was expressed in a heterologous system to levels never before achieved. The enzyme produced small partially acetylated chitooligosaccharides, which have enormous biotechnological potential in medicine and food. Chit42 3D structure was characterized and analysed. Production and understanding of how the enzymes generating bioactive chito-oligomers work is essential for their biotechnological application, and paves the way for future work to take advantage of chitinolytic activities. Electronic supplementary material The online version of this article (10.1186/s12934-018-0895-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter Elias Kidibule
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1, Cantoblanco, 28049, Madrid, Spain
| | - Paloma Santos-Moriano
- Institute of Catalysis and Petrochemistry, CSIC, C/ Marie Curie, 2, Cantoblanco, 28049, Madrid, Spain
| | - Elena Jiménez-Ortega
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (CSIC), C/ Serrano, 119, 28006, Madrid, Spain
| | - Mercedes Ramírez-Escudero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (CSIC), C/ Serrano, 119, 28006, Madrid, Spain
| | - M Carmen Limón
- Department of Genetic, University of Sevilla, Avenida Reina Mercedes s/n, 41012, Seville, Spain
| | - Miguel Remacha
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1, Cantoblanco, 28049, Madrid, Spain
| | - Francisco José Plou
- Institute of Catalysis and Petrochemistry, CSIC, C/ Marie Curie, 2, Cantoblanco, 28049, Madrid, Spain
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (CSIC), C/ Serrano, 119, 28006, Madrid, Spain
| | - María Fernández-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1, Cantoblanco, 28049, Madrid, Spain.
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Implications of molecular diversity of chitin and its derivatives. Appl Microbiol Biotechnol 2017; 101:3513-3536. [DOI: 10.1007/s00253-017-8229-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/26/2017] [Accepted: 03/04/2017] [Indexed: 02/03/2023]
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26
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Slámová K, Bojarová P. Engineered N-acetylhexosamine-active enzymes in glycoscience. Biochim Biophys Acta Gen Subj 2017; 1861:2070-2087. [PMID: 28347843 DOI: 10.1016/j.bbagen.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 01/17/2023]
Abstract
BACKGROUND In recent years, enzymes modifying N-acetylhexosamine substrates have emerged in numerous theoretical studies as well as practical applications from biology, biomedicine, and biotechnology. Advanced enzyme engineering techniques converted them into potent synthetic instruments affording a variety of valuable glycosides. SCOPE OF REVIEW This review presents the diversity of engineered enzymes active with N-acetylhexosamine carbohydrates: from popular glycoside hydrolases and glycosyltransferases to less known oxidases, epimerases, kinases, sulfotransferases, and acetylases. Though hydrolases in natura, engineered chitinases, β-N-acetylhexosaminidases, and endo-β-N-acetylglucosaminidases were successfully employed in the synthesis of defined natural and derivatized chitooligomers and in the remodeling of N-glycosylation patterns of therapeutic antibodies. The genes of various N-acetylhexosaminyltransferases were cloned into metabolically engineered microorganisms for producing human milk oligosaccharides, Lewis X structures, and human-like glycoproteins. Moreover, mutant N-acetylhexosamine-active glycosyltransferases were applied, e.g., in the construction of glycomimetics and complex glycostructures, industrial production of low-lactose milk, and metabolic labeling of glycans. In the synthesis of biotechnologically important compounds, several innovative glycoengineered systems are presented for an efficient bioproduction of GlcNAc, UDP-GlcNAc, N-acetylneuraminic acid, and of defined glycosaminoglycans. MAJOR CONCLUSIONS The above examples demonstrate that engineering of N-acetylhexosamine-active enzymes was able to solve complex issues such as synthesis of tailored human-like glycoproteins or industrial-scale production of desired oligosaccharides. Due to the specific catalytic mechanism, mutagenesis of these catalysts was often realized through rational solutions. GENERAL SIGNIFICANCE Specific N-acetylhexosamine glycosylation is crucial in biological, biomedical and biotechnological applications and a good understanding of its details opens new possibilities in this fast developing area of glycoscience.
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Affiliation(s)
- Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
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Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol 2017; 5:16. [PMID: 28337436 PMCID: PMC5343024 DOI: 10.3389/fbioe.2017.00016] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Lipases are important industrial enzymes. Most of the lipases operate at lipid–water interfaces enabled by a mobile lid domain located over the active site. Lid protects the active site and hence responsible for catalytic activity. In pure aqueous media, the lid is predominantly closed, whereas in the presence of a hydrophobic layer, it is partially opened. Hence, the lid controls the enzyme activity. In the present review, we have classified lipases into different groups based on the structure of lid domains. It has been observed that thermostable lipases contain larger lid domains with two or more helices, whereas mesophilic lipases tend to have smaller lids in the form of a loop or a helix. Recent developments in lipase engineering addressing the lid regions are critically reviewed here. After on, the dramatic changes in substrate selectivity, activity, and thermostability have been reported. Furthermore, improved computational models can now rationalize these observations by relating it to the mobility of the lid domain. In this contribution, we summarized and critically evaluated the most recent developments in experimental and computational research on lipase lids.
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Affiliation(s)
- Faez Iqbal Khan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China; School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Rabia Durrani
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Weiqian Huan
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Zexin Zhao
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
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28
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Shahbaaz M, Rahman S, Khan P, Kim J, Hassan MI. Classification and structural analyses of mutational landscapes in hemochromatosis factor E protein: A protein defective in the hereditary hemochromatosis. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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An Q, Wang F, Lan D, Khan FI, Durrani R, Yang B, Wang Y. Improving phospholipase activity of PLA
1
by protein engineering and its effects on oil degumming. EUR J LIPID SCI TECH 2017. [DOI: 10.1002/ejlt.201600110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Qun An
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Fanghua Wang
- School of Food Science and EngineeringState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Dongming Lan
- School of Food Science and EngineeringState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Faez Iqbal Khan
- School of Chemistry and Chemical EngineeringHenan University of TechnologyZhengzhouP. R. China
| | - Rabia Durrani
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Bo Yang
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Yonghua Wang
- School of Food Science and EngineeringState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouP. R. China
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Khan FI, Bisetty K, Gu KR, Singh S, Permaul K, Hassan MI, Wei DQ. Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Ke-Ren Gu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Dong-Qing Wei
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
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A functional natural deep eutectic solvent based on trehalose: Structural and physicochemical properties. Food Chem 2016; 217:560-567. [PMID: 27664672 DOI: 10.1016/j.foodchem.2016.09.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/16/2016] [Accepted: 09/03/2016] [Indexed: 11/21/2022]
Abstract
In this study, the natural deep eutectic solvents (NADESs) based on trehalose and choline chloride have been prepared to enhance the protein thermostability. The results of fourier transform infrared spectroscopy and (1)H nuclear magnetic resonance spectroscopy suggested that there were intensive hydrogen-bonding interactions between trehalose and choline chloride in TCCL3-DES and TCCL3-DES75. The physicochemical properties of TCCL3-DES and TCCL3-DES75 were investigated in the temperature range of 293.15-363.15K. Our results revealed that the thermostability of lysozyme, a model protein used in this study was dramatically increased in TCCL3-DES75, as evidenced by the disappearance of the denaturing peak from their Differential Scanning Calorimetry (DSC) traces. The results of circular dichroism (CD) experiments further demonstrated that the lysozyme in TCCL3-DES75 unfolded partially at 90°C and recovered to the initial structure at 20°C. The study suggests that TCCL3-DES75 might be a potential solvent for stabilizing proteins.
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Khan P, Shandilya A, Jayaram B, Islam A, Ahmad F, Hassan MI. Effect of pH on the stability of hemochromatosis factor E: a combined spectroscopic and molecular dynamics simulation-based study. J Biomol Struct Dyn 2016; 35:1582-1598. [PMID: 27174123 DOI: 10.1080/07391102.2016.1189359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hereditary hemochromatosis is an iron overburden condition, which is mainly governed by hereditary hemochromatosis factor E (HFE), a member of major histocompatibility complex class I. To understand the effect of pH on the structure and stability of HFE, we have cloned, expressed, and purified the HFE in the bacterial system and performed circular dichroism, fluorescence, and absorbance measurements at a wide pH range (pH 3.0-11.0). We found that HFE remains stable in the pH range 7.5-11.0 and gets completely acid denatured at low pH values. In this work, we also analyzed the contribution of salt bridges to the stability of HFE. We further performed molecular dynamics simulations for 80 ns at different pH values. An excellent agreement was observed between results from biophysical and MD simulation studies. At lower pH, HFE undergoes denaturation and may be driven toward a degradation pathway, such as ubiquitination. Hence, HFE is not available to bind again with transferrin receptor1 to negatively regulate iron homeostasis. Further we postulated that, might be low pH of cancerous cells helps them to meet their high iron requirement.
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Affiliation(s)
- Parvez Khan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India
| | - Ashutosh Shandilya
- b Department of Chemistry , Indian Institute of Technology Delhi , New Delhi 110016 , India
| | - B Jayaram
- b Department of Chemistry , Indian Institute of Technology Delhi , New Delhi 110016 , India
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi 110025 , India
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Khan FI, Nizami B, Anwer R, Gu KR, Bisetty K, Hassan MI, Wei DQ. Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens. J Biomol Struct Dyn 2016; 35:2123-2135. [PMID: 27366981 DOI: 10.1080/07391102.2016.1206837] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Previous experimental studies on thermostable lipase from Shewanella putrefaciens suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.
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Affiliation(s)
- Faez Iqbal Khan
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Zhengzhou 450001 , Henan , China
| | - Bilal Nizami
- b School of Pharmacy and Pharmacology , University of KwaZulu-Natal , Durban 4000 , South Africa
| | - Razique Anwer
- c Department of Anatomy (Microbiology) , Al-Imam Muhammad Ibn Saud Islamic University , Riyadh , Saudi Arabia
| | - Ke-Ren Gu
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Zhengzhou 450001 , Henan , China
| | - Krishna Bisetty
- d Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Md Imtaiyaz Hassan
- e Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia , New Delhi 110025 , India
| | - Dong-Qing Wei
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Zhengzhou 450001 , Henan , China
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Khan FI, Aamir M, Wei DQ, Ahmad F, Hassan MI. Molecular mechanism of Ras-related protein Rab-5A and effect of mutations in the catalytically active phosphate-binding loop. J Biomol Struct Dyn 2016; 35:105-118. [PMID: 26727234 DOI: 10.1080/07391102.2015.1134346] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Ras-related protein (Rab-5a) is primarily involved in the regulation of early endosome fusion during endocytosis and takes part in the budding process. During GTP hydrolysis, Rab5a was spotted in the cytoplasmic side of early endosomes in association with the GTP. Previous study suggested that the substitution of alanine with proline at position 30 of Rab5a reduces the GTPase activity around 12-fold, while, with arginine substitution stimulates the intrinsic GTP hydrolysis by 5-fold. Most of the other substitutions at this position show a little or no effect on the GTPase activity. In this paper, structure analysis and molecular dynamics (MD) simulation studies of human Rab5a and its mutants have been extensively carried out. The effect of binding of a non-hydrolyzable GTP analog guanosine-5'-(β, γ)-imidotriphosphate (GppNHp) with Rab5a and its mutants are described. The objective of the current study is to perform a detailed examination of structural flexibility of Rab5a and its mutants p.Ala30Pro and p.Ala30Arg using MD simulations. Our observations suggest that mutant p.Ala30Arg stabilize the protein molecule when bound to GppNHp which offers additional contacts. Despite an in silico approach, this study provides a deep insight into the impact of mutation on the structure, function, stability, and mechanism of binding of GppNHp to the Rab5a at molecular level.
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Affiliation(s)
- Faez Iqbal Khan
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Henan 450001 , China
| | - Mohd Aamir
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
| | - Dong-Qing Wei
- a School of Chemistry and Chemical Engineering , Henan University of Technology , Henan 450001 , China
| | - Faizan Ahmad
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- b Centre for Interdisciplinary Research in Basic Science , Jamia Millia Islamia , New Delhi 110025 , India
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Khan FI, Wei DQ, Gu KR, Hassan MI, Tabrez S. Current updates on computer aided protein modeling and designing. Int J Biol Macromol 2016; 85:48-62. [DOI: 10.1016/j.ijbiomac.2015.12.072] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022]
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